Related Experiment Video
Updated: Jun 18, 2026
08:03
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
Gabriel Ostlund1, Thomas Schmitt, Kristoffer Forslund
1Department of Biochemistry and Biophysics, Stockholm Bioinformatics Centre, AlbaNova University Centre, Stockholm University, SE-10691 Stockholm, Sweden. gabriel.ostlund@sbc.su.se
Nucleic Acids Research
|November 7, 2009
Summary
The InParanoid database now includes 100 species and 42.7 million ortholog groups, featuring an improved algorithm for more accurate protein comparisons. This release enhances the study of eukaryotic gene evolution and function.
Area of Science:
- Bioinformatics
- Comparative Genomics
- Evolutionary Biology
Background:
- Ortholog databases are crucial for understanding gene function and evolution across species.
- Existing ortholog databases face challenges in data standardization and comparison.
- The InParanoid project aims to provide comprehensive ortholog data for eukaryotic species.
Purpose of the Study:
- To release version 7.0 of the InParanoid database, significantly expanding its scope and improving its ortholog detection algorithm.
- To introduce standardized data formats (SeqXML and OrthoXML) for improved interoperability among ortholog resources.
- To enhance the InParanoid website for better user experience and accessibility.
Main Methods:
- Gathering proteomes from 100 eukaryotic species and Escherichia coli.
- Implementing a revised InParanoid algorithm with a two-pass BLAST approach for enhanced specificity and sensitivity.
- Developing SeqXML and OrthoXML schemas for standardized sequence and ortholog cluster representation.
Main Results:
- InParanoid v7.0 includes 100 species and 1.3 million proteins, organized into 42.7 million pairwise ortholog groups.
- The revised algorithm demonstrates improved accuracy in identifying ortholog relationships.
- New XML schemas (SeqXML, OrthoXML) are available to facilitate data exchange and comparison.
Conclusions:
- The expanded InParanoid database and improved algorithm provide a valuable resource for comparative genomics and evolutionary studies.
- The introduction of standardized XML schemas addresses the need for interoperability among ortholog databases.
- The updated website offers enhanced usability for researchers accessing ortholog information.
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
00:58Genomic DNA in Eukaryotes
Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
01:29Modern Molecular Taxonomy
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
01:24Eukaryotic Evolution
The endosymbiont theory is the most widely accepted theory of eukaryotic evolution; however, its progression is still somewhat debated. According to the nucleus-first hypothesis, the ancestral prokaryote first evolved a membrane to enclose DNA and form the nucleus. Conversely, the mitochondria-first hypothesis suggests that the nucleus was formed after endosymbiosis of mitochondria.
Contrary to the endosymbiont theory, the eukaryote-first hypothesis proposes that the simpler prokaryotic and...
Contrary to the endosymbiont theory, the eukaryote-first hypothesis proposes that the simpler prokaryotic and...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.